[med-svn] r11865 - in trunk/packages/strap/trunk/debian: . bin
Christoph Gille
christophgil-guest at alioth.debian.org
Sun Jul 22 15:53:12 UTC 2012
Author: christophgil-guest
Date: 2012-07-22 15:53:12 +0000 (Sun, 22 Jul 2012)
New Revision: 11865
Added:
trunk/packages/strap/trunk/debian/bin/strap_protein_alignment
trunk/packages/strap/trunk/debian/strap.desktop
trunk/packages/strap/trunk/debian/strap.mime
trunk/packages/strap/trunk/debian/strap.png
trunk/packages/strap/trunk/debian/strap.sharedmimeinfo
trunk/packages/strap/trunk/debian/strap.xpm
trunk/packages/strap/trunk/debian/strap_protein_alignment.1
Removed:
trunk/packages/strap/trunk/debian/Sed.sh
trunk/packages/strap/trunk/debian/bin/strap-protein-alignment
trunk/packages/strap/trunk/debian/bin/strap_util_toClustal
trunk/packages/strap/trunk/debian/bin/strap_util_toFasta
trunk/packages/strap/trunk/debian/bin/strap_util_toMultipleFasta
trunk/packages/strap/trunk/debian/bin/toXXX.sh
trunk/packages/strap/trunk/debian/man/
Modified:
trunk/packages/strap/trunk/debian/control
trunk/packages/strap/trunk/debian/rules
trunk/packages/strap/trunk/debian/strap.install
trunk/packages/strap/trunk/debian/strap.manpages
Log:
Placed all (command line utilities for alignment file conversion, html
generation, for web services) into package strap-base. Package strap
is GUI for end users.
Replaced underscore for dash in script names.
It works. Tested on Virtual Box XUbuntu
TODO: Replace dependency kalign by by neobio
Check mime types.
Deleted: trunk/packages/strap/trunk/debian/Sed.sh
===================================================================
--- trunk/packages/strap/trunk/debian/Sed.sh 2012-07-22 12:31:32 UTC (rev 11864)
+++ trunk/packages/strap/trunk/debian/Sed.sh 2012-07-22 15:53:12 UTC (rev 11865)
@@ -1,16 +0,0 @@
-
-# This script is used to generate man pages and shell scripts from a template
-# It is not part of the package build process.
-
-cat bin/toXXX.sh | sed 's|-toXXX|-toFasta|1' > bin/strap_util_toFasta
-cat bin/toXXX.sh | sed 's|-toXXX|-toMultipleFasta|1' > bin/strap_util_toMultipleFasta
-cat bin/toXXX.sh | sed 's|-toXXX|-toClustal|1' > bin/strap_util_toClustal
-chmod a+x bin/*
-
-cat man/toXXX.1 | sed 's|toXXX|toClustal|1;s|FORMAT|clustal|1;s|OUTPUT|A single file in clustal format is written.|1' > man/strap_util_toClustal.1
-
-cat man/toXXX.1 | sed 's|toXXX|toMultipleFasta|1;s|FORMAT|multiple fasta|1;s|OUTPUT|A single file in multiple fasta format is written.|1' > man/strap_util_toMultipleFasta.1
-
-
-cat man/toXXX.1 | sed 's|toXXX|toFasta|1;s|FORMAT|fasta|1;s|OUTPUT|Fore each amino acid sequence a fasta file is generated.|1' > man/strap_util_toFasta.1
-
Deleted: trunk/packages/strap/trunk/debian/bin/strap-protein-alignment
===================================================================
--- trunk/packages/strap/trunk/debian/bin/strap-protein-alignment 2012-07-22 12:31:32 UTC (rev 11864)
+++ trunk/packages/strap/trunk/debian/bin/strap-protein-alignment 2012-07-22 15:53:12 UTC (rev 11865)
@@ -1,34 +0,0 @@
-#! /bin/sh
-
-echo '\033[42m\033[37m'$0'\033[0m '
-echo "See http://3d-alignment.eu/ "
-echo
-
-. /usr/lib/java-wrappers/java-wrappers.sh
-find_java_runtime java6
-
-# Java option max heap size
-xmx=-Xmx200M
-CP=/usr/lib/strap-base/strap-protein-alignment-1.jar:
-for i in $*; do
- if [ $i != ${i##-Xmx} ]; then xmx=$i; fi
- if [ $i != ${i##-cp=} ]; then CP=${i##-cp=}":"$CP; fi
-done
-
-if [ -f /usr/bin/tm-align ]; then S3D="-s3d=tm_align"; fi
-
-
-
-echo The maximum heap size option is $xmx.
-echo To change, add a program line option like -Xmx500M
-echo which would set heap size to 500 Megabytes.
-echo
-
-EXEC="$JAVA_HOME/bin/java $xmx -cp $CP charite.christo.strap.Strap -useDebian -warnInstall=debian $S3D -a3d=mustang -aligner2=clustalw -probeWebProxy -stdout -askUpload $*"
-
-echo
-echo $EXEC
-echo
-$EXEC
-
-
Added: trunk/packages/strap/trunk/debian/bin/strap_protein_alignment
===================================================================
--- trunk/packages/strap/trunk/debian/bin/strap_protein_alignment (rev 0)
+++ trunk/packages/strap/trunk/debian/bin/strap_protein_alignment 2012-07-22 15:53:12 UTC (rev 11865)
@@ -0,0 +1,14 @@
+#! /bin/sh
+
+echo '033[42m033[37m'$0'033[0m '
+echo "See http://3d-alignment.eu/ "
+echo
+
+
+S3D=
+if [ -f /usr/bin/tm-align ]; then S3D="-s3d=tm_align"; fi
+
+
+/bin/sh /usr/bin/strap_base $S3D -a3d=mustang -aligner2=kalign -v3d=pymol -probeWebProxy -stdout -askUpload $*
+
+
\ No newline at end of file
Deleted: trunk/packages/strap/trunk/debian/bin/strap_util_toClustal
===================================================================
--- trunk/packages/strap/trunk/debian/bin/strap_util_toClustal 2012-07-22 12:31:32 UTC (rev 11864)
+++ trunk/packages/strap/trunk/debian/bin/strap_util_toClustal 2012-07-22 15:53:12 UTC (rev 11865)
@@ -1,23 +0,0 @@
-#! /bin/sh
-
-# See http://3d-alignment.eu/
-
-
-. /usr/lib/java-wrappers/java-wrappers.sh
-find_java_runtime java6
-
-# Java option max heap size
-xmx=-Xmx200M
-
-for i in $*; do
- if [ $i != ${i##-Xmx} ]; then xmx=$i; fi
-done
-
-# The maximum heap size option is $xmx.
-# To change, add a program line option like -Xmx500M
-# which would set heap size to 500 Megabytes.
-
-
-$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toClustal $*
-
-
Deleted: trunk/packages/strap/trunk/debian/bin/strap_util_toFasta
===================================================================
--- trunk/packages/strap/trunk/debian/bin/strap_util_toFasta 2012-07-22 12:31:32 UTC (rev 11864)
+++ trunk/packages/strap/trunk/debian/bin/strap_util_toFasta 2012-07-22 15:53:12 UTC (rev 11865)
@@ -1,23 +0,0 @@
-#! /bin/sh
-
-# See http://3d-alignment.eu/
-
-
-. /usr/lib/java-wrappers/java-wrappers.sh
-find_java_runtime java6
-
-# Java option max heap size
-xmx=-Xmx200M
-
-for i in $*; do
- if [ $i != ${i##-Xmx} ]; then xmx=$i; fi
-done
-
-# The maximum heap size option is $xmx.
-# To change, add a program line option like -Xmx500M
-# which would set heap size to 500 Megabytes.
-
-
-$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toFasta $*
-
-
Deleted: trunk/packages/strap/trunk/debian/bin/strap_util_toMultipleFasta
===================================================================
--- trunk/packages/strap/trunk/debian/bin/strap_util_toMultipleFasta 2012-07-22 12:31:32 UTC (rev 11864)
+++ trunk/packages/strap/trunk/debian/bin/strap_util_toMultipleFasta 2012-07-22 15:53:12 UTC (rev 11865)
@@ -1,23 +0,0 @@
-#! /bin/sh
-
-# See http://3d-alignment.eu/
-
-
-. /usr/lib/java-wrappers/java-wrappers.sh
-find_java_runtime java6
-
-# Java option max heap size
-xmx=-Xmx200M
-
-for i in $*; do
- if [ $i != ${i##-Xmx} ]; then xmx=$i; fi
-done
-
-# The maximum heap size option is $xmx.
-# To change, add a program line option like -Xmx500M
-# which would set heap size to 500 Megabytes.
-
-
-$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toMultipleFasta $*
-
-
Deleted: trunk/packages/strap/trunk/debian/bin/toXXX.sh
===================================================================
--- trunk/packages/strap/trunk/debian/bin/toXXX.sh 2012-07-22 12:31:32 UTC (rev 11864)
+++ trunk/packages/strap/trunk/debian/bin/toXXX.sh 2012-07-22 15:53:12 UTC (rev 11865)
@@ -1,23 +0,0 @@
-#! /bin/sh
-
-# See http://3d-alignment.eu/
-
-
-. /usr/lib/java-wrappers/java-wrappers.sh
-find_java_runtime java6
-
-# Java option max heap size
-xmx=-Xmx200M
-
-for i in $*; do
- if [ $i != ${i##-Xmx} ]; then xmx=$i; fi
-done
-
-# The maximum heap size option is $xmx.
-# To change, add a program line option like -Xmx500M
-# which would set heap size to 500 Megabytes.
-
-
-$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toXXX $*
-
-
Modified: trunk/packages/strap/trunk/debian/control
===================================================================
--- trunk/packages/strap/trunk/debian/control 2012-07-22 12:31:32 UTC (rev 11864)
+++ trunk/packages/strap/trunk/debian/control 2012-07-22 15:53:12 UTC (rev 11865)
@@ -11,8 +11,8 @@
Package: strap
Architecture: all
-Depends: strap-base, ${misc:Depends}, gwrite, catdoc, clustalw, kalign, tm-align, pymol, texlive-latex-base, mustang
-Recommends: muscle, mafft, t-coffee, probcons, dialign, dialign-t, amap-align
+Depends: strap-base, ${misc:Depends}, gwrite, catdoc, clustalw, kalign, tm-align, pymol, texlive-latex-base, mustang, espeak | recite
+Recommends: muscle, mafft, t-coffee, probcons, dialign, dialign-t, amap-align, chemical-mime-data
Suggests:
Enhances: clustalw, tm-align, pymol, mustang, muscle, mafft, t-coffee, probcons, dialign, dialign-t, amap-align
Description: Work-bench for comparing proteins by sequence and
Modified: trunk/packages/strap/trunk/debian/rules
===================================================================
--- trunk/packages/strap/trunk/debian/rules 2012-07-22 12:31:32 UTC (rev 11864)
+++ trunk/packages/strap/trunk/debian/rules 2012-07-22 15:53:12 UTC (rev 11865)
@@ -7,12 +7,12 @@
%:
dh $@
+D := $(CURDIR)/debian
+L := /usr/share/texmf-texlive/tex/latex
+
override_dh_auto_build:
dh_auto_build
# Only two small sty files of the huge package texlive-latex-extra are required in Strap
# Include these two files such that texlive-latex-extra can be ommitted
- mkdir -p $(CURDIR)/debian/tmp/usr/lib/strap
- cp /usr/share/texmf-texlive/tex/latex/texshade/texshade.sty /usr/share/texmf-texlive/tex/latex/vmargin/vmargin.sty $(CURDIR)/debian/tmp/usr/lib/strap
-
-
-
+ cat $L/texshade/texshade.sty > $D/texshade.sty
+ cat $L/vmargin/vmargin.sty > $D/vmargin.sty
Added: trunk/packages/strap/trunk/debian/strap.desktop
===================================================================
--- trunk/packages/strap/trunk/debian/strap.desktop (rev 0)
+++ trunk/packages/strap/trunk/debian/strap.desktop 2012-07-22 15:53:12 UTC (rev 11865)
@@ -0,0 +1,11 @@
+[Desktop Entry]
+Version=1.0
+Name=Strap protein alignments
+Exec=/usr/bin/strap_protein_alignment
+Terminal=false
+Icon=strap
+Type=Application
+MimeType=text/x-clustalw-alignment; text/x-stockholm-alignment; chemical/seq-aa-fasta;chemical/x-pdb;application/x-mfa;chemical/x-nexus;chemical/x-swissprot;chemical/seq-na-genbank;application/x-gp;chemical/seq-aa-genpept;text/x-strap-script;
+Categories=Education;Science;Chemistry;
+GenericName=Strap protein alignments
+Comment=Sequence and structure alignments of proteins
Modified: trunk/packages/strap/trunk/debian/strap.install
===================================================================
--- trunk/packages/strap/trunk/debian/strap.install 2012-07-22 12:31:32 UTC (rev 11864)
+++ trunk/packages/strap/trunk/debian/strap.install 2012-07-22 15:53:12 UTC (rev 11865)
@@ -1,6 +1,8 @@
-debian/bin/strap_util_toFasta usr/bin
-debian/bin/strap_util_toMultipleFasta usr/bin
-debian/bin/strap_util_toClustal usr/bin
-usr/lib/strap/texshade.sty
-usr/lib/strap/vmargin.sty
+debian/texshade.sty usr/lib/strap
+debian/vmargin.sty usr/lib/strap
+debian/bin/strap_protein_alignment usr/bin
+debian/strap.desktop usr/share/applications
+debian/*.desktop usr/share/applications/
+debian/strap.png usr/share/pixmaps/
+debian/strap.xpm usr/share/pixmaps/
Modified: trunk/packages/strap/trunk/debian/strap.manpages
===================================================================
--- trunk/packages/strap/trunk/debian/strap.manpages 2012-07-22 12:31:32 UTC (rev 11864)
+++ trunk/packages/strap/trunk/debian/strap.manpages 2012-07-22 15:53:12 UTC (rev 11865)
@@ -1,3 +1,2 @@
-debian/man/strap_util_toFasta.1
-debian/man/strap_util_toMultipleFasta.1
-debian/man/strap_util_toClustal.1
+
+debian/strap_protein_alignment.1
\ No newline at end of file
Added: trunk/packages/strap/trunk/debian/strap.mime
===================================================================
--- trunk/packages/strap/trunk/debian/strap.mime (rev 0)
+++ trunk/packages/strap/trunk/debian/strap.mime 2012-07-22 15:53:12 UTC (rev 11865)
@@ -0,0 +1,26 @@
+# http://wiki.debian.org/MIME/etc/mime.types http://wiki.debian.org/MimeTypesSupport
+
+
+
+chemical/x-pdb; viewer=/usr/bin/strap_protein_alignment; description=Protein DataBank Format; nametemplate=%s.pdb;
+chemical/x-pdb; viewer=/usr/bin/strap_protein_alignment; description=Protein DataBank Format; nametemplate=%s.ent;
+
+text/x-msf-alignment; viewer=/usr/bin/strap_protein_alignment '%s'; description=MSF multiple sequence alignment; nametemplate=%s.msf
+text/x-pfam-alignment; viewer=/usr/bin/strap_protein_alignment '%s'; description=Multiple sequence alignment from PFAM; nametemplate=PF%s
+text/x-stockholm-alignment; viewer=/usr/bin/strap_protein_alignment '%s'; description=Multiple sequence alignment stockholm format; nametemplate=*.sto
+
+
+chemical/seq-aa-fasta; viewer=/usr/bin/strap_protein_alignment '%s'; description=Fasta Amino Acid Sequence; nametemplate=%s.aa
+chemical/seq-fasta; viewer=/usr/bin/strap_protein_alignment '%s'; description=Fasta Amino Acid Sequence; nametemplate=%s.fa
+chemical/seq-fasta; viewer=/usr/bin/strap_protein_alignment '%s'; description=Fasta Amino Acid Sequence; nametemplate=%s.fasta
+
+chemical/seq-aa-genpept; viewer=/usr/bin/strap_protein_alignment '%s'; description=GenPept Flat File; nametemplate=%s.gp
+
+chemical/x-swissprot; viewer=/usr/bin/strap_protein_alignment '%s'; description=SWISS-PROT protein sequence; nametemplate=%s.sw
+chemical/x-swissprot; viewer=/usr/bin/strap_protein_alignment '%s'; description=SWISS-PROT protein sequence; nametemplate=%s.swiss
+chemical/x-swissprot; viewer=/usr/bin/strap_protein_alignment '%s'; description=SWISS-PROT protein sequence; nametemplate=%s.swissprot
+
+
+text/x-strap-script; viewer=/usr/bin/strap_protein_alignment -script='%s'; description=Script file for the protein alignment package Strap; nametemplate=%s.strap
+
+text/x-clustalw-alignment; viewer=/usr/bin/strap_protein_alignment '%s'; description=Multiple sequence alignment in Clustal W format; nametemplate=%s.aln
Added: trunk/packages/strap/trunk/debian/strap.png
===================================================================
(Binary files differ)
Property changes on: trunk/packages/strap/trunk/debian/strap.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/packages/strap/trunk/debian/strap.sharedmimeinfo
===================================================================
--- trunk/packages/strap/trunk/debian/strap.sharedmimeinfo (rev 0)
+++ trunk/packages/strap/trunk/debian/strap.sharedmimeinfo 2012-07-22 15:53:12 UTC (rev 11865)
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<mime-info xmlns='http://www.freedesktop.org/standards/shared-mime-info'>
+ <mime-type type="text/x-strap-script">
+ <sub-class-of type="text/plain"/>
+ <comment>Script file for Strap protein alignment package</comment>
+ <glob pattern="*.strap"/>
+ <glob pattern="*.blabla"/>
+ </mime-type>
+
+ <mime-type type="text/x-clustalw-alignment">
+ <sub-class-of type="text/plain"/>
+ <comment>Multiple sequence alignment in Clustal W format</comment>
+ <magic priority="50">
+ <match type="string" offset="0" value="CLUSTAL"/>
+ </magic>
+ <glob pattern="*.aln"/>
+ <glob pattern="*.clustal"/>
+ <glob pattern="*.clustalW"/>
+ <glob pattern="*.clustalw"/>
+ </mime-type>
+</mime-info>
Added: trunk/packages/strap/trunk/debian/strap.xpm
===================================================================
--- trunk/packages/strap/trunk/debian/strap.xpm (rev 0)
+++ trunk/packages/strap/trunk/debian/strap.xpm 2012-07-22 15:53:12 UTC (rev 11865)
@@ -0,0 +1,40 @@
+/* XPM */
+static char *strap[] = {
+/* columns rows colors chars-per-pixel */
+"32 32 2 1",
+" c #000000",
+". c None",
+/* pixels */
+"................................",
+"................................",
+"................................",
+"................................",
+"................................",
+"... ...",
+"... ...",
+"................................",
+"................................",
+"................................",
+"........... ...",
+"........... ...",
+"................................",
+"................................",
+"................................",
+"....... ...",
+"....... ...",
+"................................",
+"................................",
+"................................",
+".............. ...",
+".............. ...",
+"................................",
+"................................",
+"................................",
+"..... ...",
+"..... ...",
+"................................",
+"................................",
+"................................",
+"................................",
+"................................"
+};
Added: trunk/packages/strap/trunk/debian/strap_protein_alignment.1
===================================================================
--- trunk/packages/strap/trunk/debian/strap_protein_alignment.1 (rev 0)
+++ trunk/packages/strap/trunk/debian/strap_protein_alignment.1 2012-07-22 15:53:12 UTC (rev 11865)
@@ -0,0 +1,369 @@
+.\"" Do not edit this file. It has been generated from templateGui.1 with /usr/bin/gpp
+.TH Strap 1 "October 2011"
+.SH NAME
+
+Strap \- Graphical user interface to compare and align proteins by sequence and 3D-structure.
+
+
+.SH Synopsis
+
+.B strap_protein_alignment [\fIprotein_files\fR] [\fIalignment_files\fR]
+
+.B strap_protein_alignment -script=[\fIURL or File\fR]
+
+.B strap_protein_alignment -align="PDB:\fIid1\fR PDB:\fIid2\fR UNIPROT:\fIid3\fR PFAM:\fIPF0...\fR ... "
+
+.B strap_protein_alignment
+[\fIoptions\fR] [\fIprotein_files\fR] [\fIalignment_files\fR] [ @ \fIfile_with_list_of_protein_files\fR]
+
+
+
+.SH DESCRIPTION
+
+The free computer program Strap aligns proteins by sequence and
+3D-structure. Strap supports the simultaneous analysis of hundreds of
+proteins and integrates amino acid sequence, secondary structure,
+3D-structure and genomic- and mRNA-sequence. Using standard methods,
+alignments are computed automatically based on sequence and structure.
+Import and export of single proteins is very easy by Drag-and-Drop.
+
+.SS Home-Page
+
+http://3d-alignment.eu/
+
+http://www.bioinformatics.org/strap/
+
+.SH PROGRAM PARAMETERS
+
+.SS Protein/alignment files
+
+Strap can be started with protein files or alignment files as parameters.
+The following formats are supported: PDB, Swissprot, Embl, Genbank,
+GenPept, Fasta, multiple-Fast, Pir, ClustalW, MSF, Nexus, Prodom,
+Pfam, Stockholm and HSSP.
+
+If at least one protein file is specified, Strap will choose the
+current working directory as the project directory. Otherwise the
+project directory is requested at the beginning of the session.
+
+
+Files preceded by a \fB@\fR sign are interpreted as lists of files.
+
+\fBCurly parenthesis\fR are used for placing sequences into the same
+alignment row. At the UNIX command prompt, the parentheses need to be
+quoted. For example \fB'{'\fR \fIprotein1.seq protein2.seq\fR
+\fB'}' '{'\fR \fIprotein3.seq protein4.seq protein5.seq \fR \fB'}'\fR
+would put two proteins into the first and three proteins into the
+second alignment row. If there are more than one sequences in a row,
+only the top most sequence is displayed.
+
+
+.SS Loading of protein entries from remote databases:
+
+The command line options \fB-load="\fR\fI space separated list of
+database entries \fR\fB"\fR loads proteins or alignments given as URL
+or database-colon-id. The option \fB-load="\fR\fI ... \fR\fB"\fR also
+aligns the downloaded proteins.
+
+
+
+.SS File Compression
+
+Supported: .gz, .bz2 and .Z
+
+.SS Parts of proteins
+
+To display only a subset of a protein, a suffix is appended to the
+protein file name.
+Residue subsets are specified by an exclamation mark and a subset
+expression after the protein file. Example:
+"hslv_ecoli.swiss!20-30,50-66". Residue numbering starts with one. To
+refer to pdb-residue numbers use the Rasmol/Jmol syntax \fIPdbResNum\fR:\fIChainLetter\fR. Example: "pdb1ryp.ent!50:A-66:A".
+
+.SH OPTIONS
+
+Program options start with a dash. The values \fBtrue\fR and
+\fBfalse\fR can be abbreviated by \fBt\fR and \fBf\fR. The "=true" or
+"=t" can be ommitted. For example \fB-noSeqres=true\fR can be written
+as \fB-noSeqres=t\fR or \fB-noSeqres\fR. For most settings there is an
+equivalent check-box or choice menu in the graphical user interface.
+
+If the Web-start script http://www.bioinformatics.org/strap/strap.php
+is started, the options are given as web-variable without the leading
+dash. For example for -noSeqres include \fBnoSeqres=t\fR into the
+URL.
+
+\fB-help\fR
+
+Prints this manual
+
+\fB-manual\fR
+
+Generates a comprehensive manual for the web browser.
+
+\fB\-noSeqres\fR
+
+ Skip SEQRES lines of PDB files.
+
+\fB\-noIdentical\fR
+
+Do not load a sequence identical to an already loaded one.
+
+\fB\-dialog\fR=\fIJavaClassNameOfDialog\fR
+
+Opens a certain dialog at start.
+The class name of a dialog is the tab-text can be obtained by opening the help text.
+
+Examples: -dialog=DialogAlign or -dialog=DialogBlast or or -dialog=DialogDotPlot
+
+\fB\-script\fR=\fIURL_or_FilePath_or_ScriptText\fR
+
+Runs a script at start. See http://www.bioinformatics.org/strap/web/strap_script.html.
+Script files in the current directory should be written with a leading
+"./" like "./myScript.txt" since Strap recognizes files by the
+presence of a slash and the absence of white space and colon.
+
+Two or more script files can be given:
+-script5=\fIhttp://...../file\fR -script7=\fIhttp://...../file\fR.
+The optional number suffix defines the order of consecutively executed scripts.
+
+Script commands can be given directly. Assume there are protein files
+in PDB format loaded by Strap. The option
+-script="open_3D viewName, *"
+would display all proteins with 3D-coordinates three-dimensionally
+(See -v3d=). Scripts consisting of more than one line should be
+stored in a file and the file path or URL should be given.
+
+Example:
+
+-script2="open_3D viewName, *" -script3="3D_select $ALL" -script7="3D_ribbons on" -script8="superimpose *"
+
+\fB\-dasRegistry\fR=\fISpace-separated list of URLs of alternative DAS-registries\fR
+
+Only needed for DAS servers that are
+
+\fB\-s3d\fR=\fIJavaClass\fR
+
+Sets the Java class to superimpose proteins.
+
+A short name can be used such as "tm_align" for "Superimpose_TM_align".
+
+Example: -s3d=tm_align or -s3d=ce or -s3d=gangstaplus
+
+\fB\-a3d\fR=\fIJavaClass\fR
+
+Sets the Java class to compute structure based sequence alignments.
+
+Examples: -a3d=tm_align or -a3d=mapsci or -a3d=matt or -a3d=mustang
+
+\fB\-v3d\fR=\fIJavaClass\fR
+
+Sets the Java class to display 3D-structures.
+
+Example: -v3d=jmol or -v3d=pymol or -v3d=astex
+
+\fB\-aligner2\fR=\fIJavaClass\fR
+
+Sets the Java class for aligning two amino acid sequences. Preferably an implementation in Java because native executables take longer to start.
+Default value is PairAlignerNeoBioPROXY.
+
+Example: -aligner2=MultipleAlignerClustalW
+
+
+\fB\-alignerP\fR=\fIJavaClass\fR
+
+Sets the Java class for aligning sequences and structures.
+The default value is clustalW.
+
+Example: -alignerP=t_coffee
+
+
+\fB\-log3d\fR
+
+All 3D-commands which are sent to 3D-protein viewers are printed to stdout.
+
+\fB\-useDebian=false\fR \fB\-useDebian=true\fR
+
+If set to true, use the Debian packages for external programs rather
+than the program versions included in Strap. For example Strap would
+use /usr/bin/pymol instead of downloading and using the Pymol from
+http://www.bioinformatics.org/strap/Binaries/.
+
+\fB\-sysProxies=true\fR or \fB-probeWebProxy=true\fR or \fB-probeWebProxy=false\fR
+
+See section Web proxies.
+
+\fB\-noCache\fR
+
+ Do not use cached results of previous
+computations. This setting can be changed in the graphical user
+interface with a check-box.
+
+This setting influences the result of searches in growing
+databases. For example consider the similarity search method
+Blast. With the cache turned on, Strap would present a previously
+computed Blast result even though new sequences might have been
+published since last run.
+
+\fB\-keepFiles\fR
+
+Do not delete temp-files after the session. This is only important for
+debugging.
+
+\fB\-Xmx500m\fR
+
+This is an option of the java command and not of Strap.
+It sets the heap size to 500 Megabyte.
+
+\fB\-geometry=\fI666x333+11+22\fR
+
+Sets the size and location of the application frame to width 666,
+height 333, horizontal screen position 11 and vertical position 22;
+
+\fB\-laf=\fIlookAndFeel\fR
+
+Examples:
+
+-laf=com.sun.java.swing.plaf.motif.MotifLookAndFeel ( or short -laf=m)
+
+-laf=com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel ( or short -laf=N)
+
+-laf=com.sun.java.swing.plaf.gtk.GTKLookAndFeel ( or short -laf=G)
+
+-laf=javax.swing.plaf.metal.MetalLookAndFeel ( or short -laf=M)
+
+Also non-standard Look-and-Feels can be used. Consider tinylaf which
+can be installed as a Debian package. The following two options would
+apply tinylaf:
+
+ \fB-cp=\fR/usr/share/java/tinylaf.jar
+-laf=de.muntjak.tinylookandfeel.TinyLookAndFeel
+
+See also http://en.wikipedia.org/wiki/Look_and_feel.
+
+\fB\-toFasta\fR \fIProtein or alignment files\fR
+
+Generates a sequence file in Fasta format for each loaded protein.
+
+
+
+.SS Security
+
+\fB\-askUpload\fR[=t/f] The user is asked each time data is uploaded
+to remote servers. The user might not want unpublished sequences to be
+sent to servers.
+
+\fB\-askExec\fR[=t/f] The user is asked when an external program is
+executed. Executing native programs might be regarded as security
+risk. There is a positive and a negative list which can be edited in
+the menu "Security" of the Preferences-menu.
+
+\fB\-allowFileModification\fR According to the default policy, files
+are only modified, created or deleted if they reside in the project
+directory or if the file path contains "StrapAlign". This is to
+prevent files to be lost. With this option file modification control
+is deactivated.
+
+
+.SH ALIGNMENT FILE GENERATION
+
+With the options \fB\-toMultipleFasta\fR or \fB\-toClustal\fR or
+\fB\-toMSF\fR or \fB\-toHTML\fR or \fB\-toWord\fR, Strap can be used as a command line
+tool to generate multiple sequence alignment files. The protein or
+alignment files given in the command line are loaded and the output
+file is generated. Finally the program terminates. Prior file export, the
+proteins may be aligned:
+
+.B strap_protein_alignment [\fIalignment_files\fR] -script="align *" -toMSF
+
+
+.SS Alignment format
+
+Comma separated display options can be appended directly (!no space) after the output file name.
+
+ w=\fIresidues per line\fR Setting output width
+
+ r=\fIcolumn range\fR Example: 20-30
+
+ r=\fIresidue position range\fR Example: aProtein/10-20
+
+
+
+ The following are valid only for html and word processor output:
+
+ h=\fI%conservation\fR Residues with higher conservation are highlighted.
+
+ s=\fIschading\fR shading= black|charge|hydropathy|chemical|nucleotide.
+
+ Example: -toHTML=output.html,w=70,h=55,s=hydropathy
+
+
+
+
+
+.SS Residue annotations in HTML alignment output.
+
+Residue positions to be highlighted in the html output need to
+be defined with script commands. See option \fB\-script=\fR\fISript-file\fR.
+The script command \fInew_aminoacid_selection\fR is used to create a new
+selection object and the commands \fIadd_annotation\fR or \fIset_annotation\fR are
+used to attach information. The script may also be used to
+define the [gapped] amino acid sequences.
+
+
+.SH PROJECT DIRECTORY
+
+The project directory holds information for gaps, 3D-transformations,
+annotations and exported files. Usually, the protein files are also
+located in the project directory. The project directory path must not
+contain white space, such as "My data" or "Eigene Dateien". Therefore
+the project directory can usually not be located in the home directory
+on Windows-XP.
+
+.SH WEB-PROXY
+
+With the option \fB-probeWebProxy=t\fR, strap attempts to access the Web in
+three different ways: (1) Directly, without Web-proxy (2) With the
+settings found in the environment variable http_proxy and (3) using
+the default mechanism of Java to apply the system wide settings. With the
+setting \fB-probeWebProxy=f\fR, however, Strap will directly connect to the
+Internet. with the option \fB-sysProxies=t\fR Strap will use the
+Java-built-in mechanism to find the system wide settings, (which might
+not work properly, depending on the Java system).
+
+.SH ALIGNMENT-FILE-EXPORT
+
+Supported formats are Multiple-Fasta, ClustalW, MSF, HSSP. A
+colorized alignment with highlighted residue selections and secondary
+structure can be exported in HTML and PDF. The colorized HTML output
+can be modified in MS-Word or other text processors. The rendering
+styles of the PDF output can be stored in annotations of residue
+selections.
+
+.SH 3D-VISUALIZATION
+
+The following 3D-protein viewers are tightly linked with the alignment
+view: Pymol, Jmol, OpenAstex. The rendering styles can be stored
+within residue selections. There is a generic Rasmol like scripting
+language which can be applied to all embedded visualization software.
+If the desired effect can not be achieved with this generic commands,
+also specific commands can be associated with residue
+selections.
+
+.SH COPYRIGHT
+
+Christoph Gille \(co 1999-2012
+
+License GPL
+
+.SH "SEE ALSO"
+
+A comprehensive manual is created with the option \fB-manual\fR
+
+.BR jalview (1)
+.BR clustalx (1)
+.BR seaview (1)
+.BR boxshade (1)
+.BR pymol (1)
+.BR openastex (1)
+.BR strap-text-viewer (1)
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